The time travel angle handles a few for sure, but the finale manufacturing still disregarded that Voyager wasnt a factory ship. The finale was just another lazy slop job on their part to get the ship home suddenly and they didnt really care about the idea of completely retrofitting their ship with new armor and weapons on the fly being a laughable proposition.
Were kind of talking past each other, the point of your complaint and my complaint is the same, the writers were just lazy and constantly took narrative shortcuts.
Irregardless, for all intensive purposes, I could care less.
https://youtu.be/lMss1CeHOiM